Mutant Cure Squad
by purplefern
Summary: In the events of "The Mutation Situation", the turtles screwed up and dumped mutagen all over the city, mutating Mr. O'Neil and also many others. But now that Donnie finally has the retro-mutagen, he can finally help all of those that they hurt. And also keep a very important promise... (Canon divergent, a Season 2 fix-it fic)
1. Chapter 1: Prologue

_So, this story was born when I re-watched TMNT 2012, and realized that the S2 plot of the turtles accidentally mutating a bunch of people was kinda dropped. And, I can't help but care about side characters, especially since a lot of the people mutated were mostly just innocent civilians. So, this is my fix-it fic where Donnie actually uses the retro-mutagen to fix the turtles' old mistakes._

* * *

After Mr O'Neil had been brought to his home (and the turtles had left April to explain everything to the still-confused and recently de-mutated man), the brothers had called the night a mostly-success and had headed to their own home.

"Dudes" said Mikey around a yawn, "I am so tired. It's not easy being Turflytle all night. Buzz buzz" he ended halfheartedly.

It was a credit to how tired Raph was too that he didn't even attempt to retaliate to "Turflytle's" annoying buzzing. All of the turtles seemed exhausted from the long night of battling Foot bots and apparently now mutated Baxter Stockman. All of the turtles except for Donnie, whose face was stretched in a wide grin as he practically bounced around the Lair.

"Retro-mutagen!" he exclaimed, elated, "I actually managed to create _working_ retro-mutagen! I _cured_ Mr O'Neil!"

"We know, Donnie," snapped Raph tiredly from where he had collapsed into the beanbag in the pit, "We were there".

Raph's biting comment did little to dent Donnie's excitement, and he kept his beaming smile as he practically dashed towards his lab. Leo watched the scene with a proud smile for all his little brother had accomplished, and at how much joy it brought him. There were few greater things that an older brother could wish for their younger siblings. All the same, he knew that Donnie must have been as exhausted from everything as the rest of them.

"Look, I know this was a big night, but I think we should all try and get some sleep" the leader suggested with a particular glance shot at the thrilled scientist.

"I agree with Leo" added Mikey with a tired raised hand from where he had laid face-down on the floor.

"Sleep? Now? Are you kidding?" gasped Donnie, "This is the scientific breakthrough of a lifetime, it could be my greatest accomplishment! I can't _sleep_ , I need to record everything about the retro-mutagen! I could-" his sentence cut off, and for the first time in the night his excitement seemed to dim as he got a thoughtful and distant look in his eyes, "I could even start making more retro-mutagen". His gaze drifted to the open doors of his lab, and his distant expression turned somber.

"Timothy" he said softly, as the full weight of what his discovery could mean finally hit him, more than just the thrill of making something new or solving a difficult chemical problem. He realized that with the retro-mutagen, he could finally make up for his biggest mistake, his biggest failure. He could keep the promise he had made.

He resumed his dash into his lab, but this time was fueled by determination rather than excitement. His brothers watched, wondering whether they should follow him or just go to bed. Sighing, Raph, ever the protective brother, reluctantly got up from his place on the beanbag and followed Donnie into his lab. Leo followed seconds after, and Mikey tagged along right behind him.

They all found Donnie standing in front of the container that held his once-human protégé, his hand placed on the ever-cool glass as he stared into the mutant's still-fierce expression. It had been months, and his frozen form still showed no signs of thawing. Surprisingly gentle, Mikey pulled his taller brother into a side-armed hug, as Raph and Leo stood comfortingly close by.

"It's ok, D" he said reassuringly while holding Donnie a little closer, with utmost confidence in his genius brother, "You can cure him now, it's all gonna be fine!"

Slowly, Donnie brought his own arm around his only little brother's shell, responding just as slowly and thoughtfully, "You're right, Mikey. I can"

"In fact," he added, finally tearing his gaze away from the ex-human, to glare determinedly around the room, "Now I can help anyone who has been mutated by the Kraang. All those people who were affected by mutagen, who maybe even lost their minds to it like Mr O'Neil or Timothy. We can help all of them! I mean, you said there was a list, right, Leo?" He turned to Leo, his eyes silently asking him to agree, to help him with this mission.

"You bet Donnie", the leader in blue responded without hesitation, "Spilling that mutagen all over the city is still our mess, and we still have to clean it up. And now we don't have to just grab the canisters of mutagen before they hurt people, we can actually help those affected".

Raph spoke up, interrupting what was sure to turn into a dramatically heroic Leo-speech fueled by fatigue, "Um, hate to sound like a jerk-"

"Since when has that ever bothered you?" quipped Mikey effortlessly.

Raph didn't justify the comment with a response, and instead barrelled on with his own comment, "But don't most of the guys that mutated _want to kill us_? _Why_ should we help them?"

"Most of the ones that want to kill us want to kill us because it's our fault they got mutated in the first place" countered Donnie, with another glance towards where the Pulverizer sat frozen with a vicious expression. "It's the right thing to do, Raph".

"And anyway" added Leo, slightly annoyed that his big speech had been cut short, "Wouldn't you rather deal with a human trying to kill you than a mutant?"

Raph blinked, processing the idea. "Yeah," he replied after a moment of thought, "I can't argue with that".

"Alright, boys!" cried Mikey, releasing Donnie from the hug to jump up onto the counter, posed heroically. "Time to cure the world! We should totally come up with a cool name! Like, Mutant Busters! Or The Cure Squad! Or, Or-!"

"Yeah!" cried Donnie, just as pumped, but showing it less enthusiastically then the energetic younger turtle, "We'll cure them all! Innnn about three months". The brothers all turned to stare at Donnie, who now seemed to be radiating faux excitement, probably trying to keep morale up. At their questioning stares, he cleared his throat and clarified. "Retro-mutagen takes months to properly synthesize. Plus I need to track down more mutagen in order to make it. But don't worry, now that I know what to do to make it it should only take about" he ran some quick calculations, "Two months and fifteen days instead of the nearly five months it took the first time":

"Duuuude" complained Mikey, his posture deflating with disappointment, "You got me all hyped to be a Mutant Cure Squad! Now I gotta wait two months?!"

"I mean, seriously" also complained Raph, "Can't you make it any quicker? Your and Leo's lame speeches actually got me all pumped, and now I have to wait? What are we supposed to do for two months?"

"Well," suggested Donnie, "We do still have to collect all of the remaining mutagen canisters. Plus we need to find the mutants to cure them. I mean, we haven't seen most of these guys since we first met them".

"That's true" added Leo, starting to count on his fingers, "Spiderbytez, the Squirrelinoids, Dr Rockwell, Snakeweed. Who _knows_ where those guys are!"

"Man," commented Mikey offhandedly, "We sure mutated a lot of people".

"Ok, fine" growled Raph, "We'll keep looking for mutagen , in two months-"

"And fifteen days" interjected Donnie.

Huffing, Raph continued, "In two months and fifteen days we take the retro-mutagen with us and we de-mutate them all".

"Alright!" cried Mikey, flipping off of the counter and back to the ground, "The Mutagen Cure Squad is a-go!"

Two Months (and fifteen days) Later…

"Guys!" shouted Donnie from inside of his lab, "I finally got it!"

Everyone immediately halted in their activities, and ran towards Donnie's lab, where he was proudly holding up a half-filled beaker of red-orange ooze of retro-mutagen.

"Wooooww" admired Mikey, "I mean, I know you made this before, but now it's even cooler because I know what it does!"

"That's all there is?" questioned Raph, eye ridge raised skeptically.

Glancing down at the half-filled container, Donnie shrugged, and replied, "Well, yeah. But it only takes a drop to work, we learned that from Mr O'Neil. This should be more than enough, as long as we use it sparingly" he stressed with a special glare shot at the youngest brother, who had leaned over the counter to look at the retro-mutagen more closely. Mikey laughed guiltily, and immediately backed away from the counter.

"So,um, Donnie," said Leo hopefully, "Does this mean you can help the Pulverizer now?"

Unexpectedly, Donnie, instead of looking excited or hopeful, glanced aside and sighed. "I wish I could, but unfortunately, " he gestured widely at the frozen mutant behind them, "Timothy is still frozen solid. I can't know how that would affect his de-mutation. It could kill him for all I know! Before I cure him of his mutation, I need to find a way to thaw him out".

"Oh," responded Leo, shifting awkwardly before laying a comforting hand on his purple-banded brother's shoulder. "Well, that can't be as hard as making a retro-mutagen, right?"

"Yeah, D" added Mikey cheerily, throwing his arm around Donnie's shell, "If anyone can figure it out, you can!"

"Indeed, my son," the turtles all jumped slightly at the sudden presence of their father. "With your knowledge, I am sure you will be able to keep your promise".

Donnie smiled shyly at the praise. Though Splinter was far from a cruel father, praise was something he gave only when he felt it was truly deserved. "Thanks Sensei".

"In the meantime," he addressed to all of them in a more serious tone, "there are many other mutants that still need to be cured".

"Sensei is right" added Leo, arms now crossed over his plastron in attempt to look more serious, "We need to start tracking them all down to de-mutate them".

"So where do we start?" asked Raph, his sai clenched in his fist.

"I seem to remember a group of dangerous squirrels attacking our home," suggested Splinter with a slight tone of chastisement, "Perhaps it is time you took care of that problem".

Leo laughed nervously, before replying, "Hai, Sensei".

Nodding in approval, Splinter laid a reassuring hand on Donnie's shoulder, saying, "You have done a great thing, my son. Now " he continued, releasing his genius son's shoulder and once again turning to all of his sons, "Go help the other mutants". The turtles bowed in agreement, and with that, the Sensei turned and left the room, leaving the team to plan their mission.

Straightening once Splinter had left the room, the teens all turned to each other.

"Well, you guys heard Sensei. We're going on another squirrel hunt," said Leo in an authoritative voice.

"Um, excuse me, Squirrelinoids," corrected Mikey, "Also, uggghhhh," he cried, "We have to try to _find_ the Squirrelinoids?! I _hate_ those things!"

"Suck it up, Mikey", grunted Raph, rolling his eyes.

"Alright," said Donnie, already bustling around his lab to prepare for their mission, looking from shelf to shelf, "I think I can find a good way to distribute the retro-mutagen. But first things first," he paused in his searching to look at his brothers seriously, "I need to to lay some ground rules". His brothers, except for Leo, quietly groaned.

"This is important, guys," he stressed, "Okay, rule one, and this is the most important rule, be _very careful_ with the retro-mutagen. DO NOT let it touch you. I'm working on making us all special gloves to minimize our risk of exposure. If we come into physical contact with this it would essentially **kill us** , removing the mutations that give us sentience and turning us into normal turtles. Do you all understand?" Donnie stared them all down fiercefully, even his older brothers, even the leader of the team. They were all slightly taken aback by the commanding attitude Donnie had. But they all nodded in understanding.

Donnie seemed to deflate with relief, glad that he had conveyed the seriousness of the first rule. He continued, in a more normal lecturing tone that immediately set his brothers at ease with its familiarity, "Ok, rule number two, while less imperative than the first, is still important to keep in mind. This" he gestured to the beaker of red-orange ooze, "is all the retro-mutagen we have for now. As you know, it takes a while to make more, plus, you know, I'd need April's blood to make it, so use it sparingly. Additionally, it only takes a drop to properly cure something, so don't go crazy with it unnecessarily".

"Third, and I don't think you guys will like me for this, as long as the mutant is sentient, it should ultimately be _their choice_ whether they want to be cured or not".

"What?! Donnie, you can't be serious!" yelled Raph, "Do you even realize how many of those dangerous freaks want to kill us? And you want to let them?!"

"I kind of agree with Raph on this one," added Leo reluctantly, "It seems like it would be more sensible to change the more dangerous mutants human, whether they want it or not".

Shaken, but still holding firm to his ideals, Donnie shook his head and explained, "It's just not right though, Leo. We're trying to use this cure to help people. If the mutant is fully cognizant and consciously prefers to be a mutant, who are we to say they can't?" Donnie took a deep breath, reminding himself of why he decided to set this rule, and reassuring himself that it was the right thing to do.

"That's the rule, and I'm sticking to it. At any rate," he added in a lighter tone, "it's highly unlikely that any of the mutants that were originally humans would even _want_ to stay as mutants. And any of the sentient ones that used to be animals we can't 'cure' for obvious ethical reasons".

Raph scoffed fondly at his idealistic younger brother, "Donnie, you're such a moralizer. But, I guess you _are_ right. Even if he's dangerous, I don't know how good I would feel about turning Spike back into an ordinary turtle".

"So are those all of the rules?" asked Leo.

"Um" replied Donnie, counting on his fingers and going back over the rules, "Yeah, I guess that's it".

"Whew" sighed Mikey in relief, "Only three rules. I think I can handle remembering that".

"I hope so," said Leo, "because we're going after those Squirrelinoids as soon as Donnie gets the retro-mutagen ready. It's about time we got those dangerous creatures out of the sewers, and stop them from hurting anyone for good".

"Mutant Cure Squad is a-go! Again!" cried Mikey enthusiastically.

* * *

 _So, that was the prologue. Hopefully pretty good so far. For once I have these chapters written ahead of time, so hopefully this fic doesn't fall into the massive hiatuses my fics are usually prone to. R &R, until next chapter. _


	2. Chapter 2: Squirrelanoids

_What's this? A chapter that was updated just about a week after the first? As if there is some kind of schedule? 1 for 1 on weekly updates, nice!_

* * *

 **Chapter 2: Squirrelinoids**

"Remind me again why the squirrelinoids were our pick for first mutant to go after?" grumbled Raph from his place at the back of the pack as the turtles searched deeper and deeper through the dark sewer tunnels.

"Because" replied Leo while scanning the dark for any signs of mutant activity, "they're a potential danger to civilians, and we've put off this problem for long enough. Also Splinter told us to."

"Yeah, Raph," inputted Donnie, briefly looking up from the mutagen scanner to fiddle with the syringe he had partially filled with retro-mutagen, "Did you expect flushing them down the sewers to magically solve the problem? It's not like they drowned or anything. They're probably still wandering around somewhere".

"What?!" exclaimed Mikey, "You're telling me my genius plan didn't actually work? But it worked in my comic!"

"Yeah, but in your comic the aliens were flushed into _space_ ," sighed Donnie, "where there's _no oxygen_? The sewers wouldn't exactly kill them, just...hold them for a little while".

Mikey silently pouted as they turned down another tunnel, following Donnie's lead as his scanner searched for any trace of the rogue mutants. The dank tunnels were quiet except for the beeping of the mutagen scanner, and the distant trickle of water. It seemed like nothing could live down in the man-made depths, let alone monster squirrels, until the illusion was shattered by the occasional darting rat brushing against their feet. They had been wandering down here going further and further from the surface for nearly two hours, and so far the search had been a bust.

"I'm just saying" continued Raph, breaking the heavy silence of the lifeless underground, "Couldn't we have chosen a mutant that was less dangerous? Or that was above ground? Or that wasn't a crazy murdering monster that could suddenly attack us out of the dark and we would have like no room to defend ourselves?"

"Raphael" teased Leo, glancing back from where he stood just behind Donnie to smirk at his younger brother, "Are you telling me that you're scared?"

"I'm not scared! Who said I was scared? These are totally rational, not-at-all fear-fuelled questions", Raph vehemently denied.

"It's alright, dude" comforted Mikey, "I'd be scared of mutant monsters that had replicated inside of my stomach, too".

Fortunately for Raph, the darkness hid his sickened expression, and how his face turned a little more green than usual, "Not helping, Mikey!"

"Guys, stop it" snapped Donnie, briefly looking up from his scanner to pin his brothers with a criticizing glare, "I can barely hear my scanner with all of your arguing!"

"Who cares?" complained Raph, glad to be off the subject of his supposed fears, "Even with you being able to hear it, we've been at this for two hours for squat! We haven't found anything!"

Donnie opened his mouth to reply, but was interrupted as the beeps on the scanner grew quicker and more frequent.

"Looks like the hunt is on" he said instead, continuing on in the direction of the beeping scanner.

"And it wasn't on before because….why?" grumbled Raph, both still scared and glad to finally be able to deal with fear the way he knew best: punching it.

Ignoring Raph (which had become the norm in the last half hour), Leo turned to everyone and tried to turn the mood more serious. "Ok, everyone, here's the plan (since it _has_ been like forever since I last said it)," Donnie couldn't help glaring at the subtle jab, "Donnie has the retro-mutagen, so me, Raph, and Mikey will try to incapacitate the Squirellinoids, and then Donnie will spritz them with some of the retro-mutagen. Everyone needs to be _extremely careful_ while that happens, unless you want to spend the rest of your life being fed pellets in an aquarium. On that note, everyone got their gloves?"

"Yes, sir" replied Raph in a mocking salute, "For all the good that will do."

"I'm still working on something more protective, but for now it's better that you have the gloves than nothing" said Donnie, as the team pulled on pairs of specially made for mutant turtle hands, elbow-length gloves. Mikey couldn't help but giggle at the comically-large length of them. "They look like something from some super-cheesy sci-fi show".

Leo continued, "Alright. Raph, got your rope?"

"Yup," he replied, twirling the hooked end of his grappling line.

"Mikey, do you have your kusarigama?"

"C'mon Leo, I'm not _that_ dumb. Of course I've got'em!"

The group stopped as the tunnel they were in reached a larger chamber, and the beeps became so frequent that one could hardly be distinguished from the other. All at once, their posture straightened, and they looked less like a disorganized group of teenage brothers, and more like a skilled and deadly team of ninja. Donnie quickly turned off the scanner and tucked it in his belt. Sending a quick nod towards the rest of the team, he slipped into step behind them, and they all silently moved into the chamber.

The three mutated squirrels were restlessly sleeping in the center, curled up on a mess of garbage of chip bags, shopping bags, ripped up cloth of unknown origin, and various bodies of small birds and cats. Their dinners. Mikey stifled a small gasp at the sight of the mutant nest.

With a quick glance around the room, Leo confirmed that all three of the squirrelanoids were there, and signaled to the incapacitating-team. Each brother flanked out to take down a mutant-squirrel each. Leo counted down on his fingers, and at zero all three of the teens quickly and stealthily threw ropes or chains around the napping mutants. Instantly, the killer squirrels shot awake, and thrashed in attempts to throw off the binds. Leo, Raph, and Mikey held tough, wrapping the chains around their wrists for better grip, and leaning against the squirrelinoids with all of their strength.

"Any time now, Donnie!" shouted Raph as he tugged the fighting squirrel mutant back.

Not wasting time or breath on a response, Donnie pulled off the safety cap of the retromutagen, and dashed towards the one Mikey held, the most likely one to break free first. Taking an extra careful second to aim, so as not to accidentally hit his younger brother, Donnie spritzed the struggling mutant before immediately moving on to the next one. One after another the raging rodents were sprayed with the cure for their monstrous mutations, and they all struggled harder, but as their elongated limbs shrunk back into place and their fur grew back in patches, the squirrels gradually calmed down. After a brief moment, all of the brothers let out a relieved breath as the sewer tunnel was left with nothing more dangerous than three scampering, normal squirrels.

"Aw, yeah, boi!" cried Mikey in victory, sharing a cheerful high-three with each of his brothers, "The Mutant Cure-Squad was a success! Let's get pizza to celebrate!"

"Just let me do one thing first" said Donnie, carefully approaching the wandering critters with a cat carrier in his hand. He quickly herded the still somewhat disoriented squirrels into the carrier, and then turned back to his brothers. "Ok, now we can go".

The brothers headed up to the surface to get some Antonios, joking and playfully shoving each other, but Donnie hung back a bit. Pausing for a moment, he opened up the carrier and nudged the squirrels out. The normal, harmless, _cured_ animals paused only a moment to sniff the air, before running off down the alley, back into the city. Donnie smiled to himself, proud and glad to have gotten rid of one more danger in the already dangerous town, then ran to catch up with his brothers.

Tonight they would celebrate, but he knew there was a lot more work to do.

* * *

 _So, anyway, this was the first real chapter of this story. R &R, until next chapter. _


	3. Chapter 3: Snakeweed

**Chapter 3:Snake (Snakeweed)**

Donnie tucked and rolled as a large vine was shot at his face, narrowly avoiding crashing into the wall of the alley. The turtles had succeeded in finding Snakeweed, but reasoning with him was proving to be a lot harder. "Please, calm down! We're not here to fight you, I swear!" pleaded the brainy turtle as he had to dodge another attack.

"Um, Donnie" yelled Raph as he impaled an attacking vine, ripping it off with a squelch,  
"In case you haven't noticed, talking isn't working! Let's just spray him already and go home!"

"Yeah!" agreed Mikey as he attempted to wrap a chain around the flailing mutant, "I don't think he _wants_ to stay a walking salad".

Donnie shifted uncomfortably, still holding his bo out in a defense position, and considered. "I'd really like another moment to either get consent, or verify that he's incapable of giving it".

"Donnie", reasoned Leo in as level a voice he could manage, "He hasn't said a coherent word the whole time we've been here, and he went straight into attacking us as soon as we showed up. I don't think he's thinking the most clearly right now".

A squealing shriek from the plant mutant reinforced Leo's argument, and made Donnie feel guilty that his brother was probably right. Even if Snake had been a criminal, he couldn't help but feel bad that they caused him to lose his mind. Steadying his nerves, Donnie got serious, taking out the sprayer of retro-mutagen and popping the safety cap off. His brothers all sighed in relief that the fight would be over soon. (Not that fighting Snakeweed was normally that difficult, but it was when you had strict orders to not completely cream him.)

"Ok, Snake, I'm going to ask one last time to be sure. I have the cure for your mutation right here, should I use it?" Snakeweed gave no indication that he heard or understood the question, and continued to whip vines around, which all of the turtles had to dodge.

"Good enough answer for ya, Donnie?" asked Raph testily.

Deciding once and for all that Snakeweed was irrational, Donnie aimed the retro-mutagen and sprayed. Fortunately, Snakeweed was a pretty large target, so that made him hard to miss. It was nice to have an easy one for once, just spray in the general direction and that's it.

When the shot hit its mark, Snakeweed flailed more erratically, a harsh scream coming from the giant plant. Little by little, starting at the head and going downwards, the plant flesh turned a deadish white-gray, and fell to the ground in clumps. Soon, a hand emerged from the pile of leaves and stem, and was soon followed by the head and torso of a raggedy tan-skinned man. Snake blinked, and stared forward dazedly, before bringing his hand in front of his face, wiggling his fingers in wonder.

Clearing his throat awkwardly, Donnie moved to offer his hand to help the recently cured human up, saying, "Um, Mr Snake, sir-" Snake's head snapped up, and for a moment his features warred between relieved joy and anger, before settling on anger.

"You turtles!" he screamed, rage winning over his continued wonder at having his normal voice back, "Get away from me!" he scrambled backwards through the remains of his old body.

Leo, a more assertive negotiator than the gentle Donnie, stepped up to calm the situation, "It's ok, Snake, it's all over, my brother cured you".

"You're welcome for that by the way" cut in Raph brusquely, not forgetting that they met Snake when he was kidnapping people.

"Yeah, well, it's _you freaks_ ' faults I was a mutant in the first place!"

Both Raph and Leo had a response for that, when surprisingly Donnie stepped up, looking down at the human sternly, "Don't give us that. You were kidnapping people. We just did what we had to do to rescue your victims".

"You know what they say about karma" chirped Raph sassily with a smirk.

"Yeah!" added Mikey, feeling somewhat left out. In an aside to Leo, he asked, "Wait, what _do_ they say?"

Amusedly rolling his eyes at his innocent little brother, Leo turned back to Snake, who despite his anger had not moved. "Look, Snake, you did something bad and got turned into a plant because of it. But now you're human again. Consider it a second chance".

The leader turned back to his team, their mission finished, "C'mon guys, let's go".

Raph gave a sassy wave to the thoughtful/angry Snake, snarking, "See ya, but not really", before turning and following Leo back up to the rooftops. Donnie gave the ex-mutant a meaningful look, before he too climbed up the nearest fire-escape, his little brother in tow.

Back on the roofs of New York, the turtles all watched as Snake stared after them with an unreadable expression from where they were, then shakily got to his feet and walked away, not looking back at the remains of what had he had been.

"Do you think he'll take this second chance to heart?" Donnie couldn't help but wonder out loud.

"Pssh, doubt it. Criminals don't change" answered Raph, already turning away and ready to go home.

"I don't know, dude" answered Mikey more thoughtfully, "I mean, I kinda hope so. Anyone can change, right?"

Donnie looked at his brother in surprise, but then turned thoughtful as well. "I guess so, Mikey". With that one more wrong righted, the turtles turned towards home.

* * *

 _know this isn't the super duper interesting or emotional stuff yet, but I promise, we're building up to that. I just really want to cure some people, or, well, all the people. R &R, until next chapter. _


End file.
